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Supplementary Table 5. Abundance of Gut Microbes in the ND-FMT And

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BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s) Gut Supplementary table 5. Abundance of gut microbes in the ND-FMT and HFD-FMT mice Mean Mean ND-FMT HFD-FMT abundance abundance Taxon Bacteria P-value ND- ND- ND- ND- ND- HFD- HFD- HFD- HFD- HFD- in ND-FMT in HFD- FMT-1 FMT-2 FMT-3 FMT-4 FMT-5 FMT-1 FMT-2 FMT-3 FMT-4 FMT-5 (%) FMT (%) Acidobacteria 0.04524 0.00179 0.023 0.00978 0 0 0 0.03273 0 0 0.0159612 0.0065458 0.1812205 Actinobacteria 0.04298 0.06254 0.15893 0.10953 0.1002 0.07086 0.06584 0.20766 0.04915 0.04967 0.0948348 0.0886348 0.8412698 Bacteroidetes 54.9036 40.8262 64.2605 42.7708 44.4954 52.5744 39.4296 48.1604 44.3388 36.521 49.451308 44.204844 0.4206349 Chlamydiae 0 0 0 0 0 0 0 0.00113 0 0 0 0.0002258 0.4237108 Chlorobi 0 0 0.00418 0 0 0 0 0 0 0 0.0008364 0 0.4237108 Chloroflexi 0.03845 0 0.023 0 0 0 0 0.01354 0 0 0.0122906 0.0027086 0.440686 Cyanobacteria 0.13119 0.52891 0.54579 0.35207 0.56496 0.28173 0.21358 0.63765 0.64078 0.51145 0.4245826 0.4570396 0.8412698 Deferribacteres 0.00226 0.02502 0 0.01565 0.0064 0.00337 0.00161 0.02144 0.00189 0 0.0098644 0.0056626 0.4633439 Bacteria; 42.6129 57.6281 32.7889 53.64 52.6287 44.9322 58.0412 48.2383 51.5972 61.2345 47.859723 52.808673 0.547619 Phylum Gemmatimonadetes 0.01131 0 0 0.00196 0 0 0 0.02257 0 0 0.002653 0.0045144 0.7971697 Nitrospirae 0 0 0 0 0 0.00506 0 0 0 0 0 0.0010122 0.4237108 OD1 0 0.00179 0 0 0 0 0 0 0 0 0.0003574 0 0.4237108 Planctomycetes 0.00679 0.00536 0.04391 0.02347 0 0.00675 0.00161 0.01693 0.00189 0.00184 0.0159062 0.0058026 0.4206349 Proteobacteria 1.84339 0.43421 0.58343 1.87185 1.21093 1.28045 1.39547 1.43444 1.89211 1.18664 1.1887608 1.4378216 0.547619 Spirochaetes 0.00226 0.00179 0 0 0 0 0.00161 0 0 0 0.0008098 0.0003212 0.440686 TM7 0.00226 0.00357 0 0 0.00213 0.10122 0.01124 0.0237 0.07372 0.00184 0.0015936 0.042344 0.0593271 Tenericutes 0.09952 0.15903 1.17522 0.33056 0.71846 0.08941 0.04657 0.02483 0.72962 0.00736 0.4965562 0.1795584 0.0952381 Verrucomicrobia 0.15154 0.21442 0.24885 0.75891 0.18548 0.52298 0.67124 1.03605 0.55194 0.27412 0.3118396 0.6112658 0.0952381 WPS-2 0.00226 0 0 0 0 0 0 0 0 0 0.0004524 0 0.4237108 Acidobacteria-6 0.03845 0.00179 0.00837 0.00978 0 0 0 0.02822 0 0 0.0116766 0.005643 0.1812205 Solibacteres 0.00679 0 0 0 0 0 0 0 0 0 0.001357 0 0.4237108 Sva0725 0 0 0.00837 0 0 0 0 0 0 0 0.001673 0 0.4237108 iii1-8 0 0 0 0 0 0 0 0.00451 0 0 0 0.00090280.4237108 Acidimicrobiia 0.00452 0 0.02509 0 0 0 0 0.00226 0 0 0.0059236 0.0004514 0.440686 Actinobacteria 0.01131 0.0143 0.03555 0.04694 0.0064 0.02531 0.00964 0.09029 0.00189 0.0092 0.0228984 0.0272632 0.6904762 Coriobacteriia 0.02488 0.04646 0.02928 0.05868 0.09167 0.03205 0.0546 0.05643 0.04348 0.04048 0.0501932 0.0454062 1 Class MB-A2-108 0 0 0.00209 0.00391 0 0.00169 0 0.01242 0 0 0.0012006 0.0028204 1 Rubrobacteria 0 0 0.02509 0 0 0.00675 0 0 0.00189 0 0.0050188 0.0017276 0.7971697 Thermoleophilia 0.00226 0 0.04182 0 0.00213 0.00506 0.00161 0.04627 0.00189 0 0.0092434 0.0109658 0.8325188 Bacteroidia 54.8516 40.7923 64.227 42.7219 44.4314 52.5339 39.367 48.1141 44.2821 36.4254 49.40485 44.144492 0.4206349 Cytophagia 0.01131 0.00715 0.00627 0.00587 0.01279 0.00506 0.00964 0.00564 0.00189 0.0184 0.0086778 0.0081254 0.4206349 Flavobacteriia 0 0 0 0 0 0 0.00161 0.00113 0.00189 0.00184 0 0.001293 0.0253699 Sphingobacteriia 0.00679 0 0 0 0 0 0 0 0.00189 0.00368 0.001357 0.001114 0.7971697 Ding N, et al. Gut 2020; 69:1608–1619. doi: 10.1136/gutjnl-2019-319127 BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s) Gut Chlamydiia 0 0 0 0 0 0 0 0.00113 0 0 0 0.0002258 0.4237108 OPB56 0 0 0.00418 0 0 0 0 0 0 0 0.0008364 0 0.4237108 Anaerolineae 0.03167 0 0 0 0 0 0 0.01016 0 0 0.00633320.0020314 1 Chloroflexi 0.00226 0 0.00209 0 0 0 0 0 0 0 0.0008706 0 0.1797125 Ellin6529 0 0 0.01255 0 0 0 0 0 0 0 0.0025094 0 0.4237108 Gitt-GS-136 0 0 0.00627 0 0 0 0 0.00339 0 0 0.0012546 0.0006772 1 TK10 0 0 0.00209 0 0 0 0 0 0 0 0.0004182 0 0.4237108 Thermomicrobia 0.00452 0 0 0 0 0 0 0 0 0 0.0009048 0 0.4237108 4C0d-2 0.12666 0.52891 0.5416 0.35012 0.5607 0.27836 0.21036 0.63765 0.64078 0.50409 0.4215974 0.4542506 0.8412698 Chloroplast 0.00226 0 0 0 0.00426 0 0.00321 0 0 0 0.0013052 0.0006424 0.6072355 Oscillatoriophycide 0 0 0 0 0 0 0 0 0 0.00184 0 0.0003680.4237108 Deferribacteres 0.00226 0.02502 0 0.01565 0.0064 0.00337 0.00161 0.02144 0.00189 0 0.0098644 0.0056626 0.4633439 Bacilli 0.02262 0.00715 0.01882 0.01565 0.0064 0.0388 0.21679 0.10496 0.0775 0.0184 0.0141258 0.091289 0.031746 Clostridia 42.5495 57.5834 32.7618 53.6068 52.5157 44.7669 57.6157 48.1006 51.4857 61.2124 47.803437 52.636241 0.547619 Erysipelotrichi 0.04071 0.03395 0.00418 0.01369 0.10446 0.12484 0.20234 0.02709 0.02646 0 0.0394002 0.0761448 0.8412698 Gemm-5 0.00226 0 0 0 0 0 0 0 0 0 0.0004524 0 0.4237108 Class Gemmatimonadetes 0.00905 0 0 0.00196 0 0 0 0.02257 0 0 0.0022006 0.0045144 0.7971697 Nitrospira 0 0 0 0 0 0.00506 0 0 0 0 0 0.0010122 0.4237108 ABY1 0 0.00179 0 0 0 0 0 0 0 0 0.0003574 0 0.4237108 OM190 0 0 0 0 0 0 0 0 0.00189 0 0 0.0003780.4237108 Phycisphaerae 0.00452 0.00357 0 0.00391 0 0 0 0 0 0 0.002402 0 0.0720057 Planctomycetia 0.00226 0.00179 0.04391 0.01956 0 0.00675 0.00161 0.01693 0 0.00184 0.0135046 0.0054246 0.6004018 Alphaproteobacteria 0.04524 0.01966 0.04391 0.02543 0.01919 0.01687 0.01606 0.01467 0.00189 0.0092 0.030684 0.0117378 0.0079365 Betaproteobacteria 0.0181 0.01072 0.01046 0.05868 0.02132 0.02531 0.00642 0.08239 0.00189 0.00184 0.023854 0.023569 0.547619 Deltaproteobacteria 0.87533 0.37345 0.48305 1.6606 1.09368 1.19104 1.3489 1.10376 1.88077 1.16641 0.8972226 1.3381744 0.0952381 Epsilonproteobacter 0.00452 0.00715 0.01464 0.09193 0.02558 0.0135 0.00642 0.21669 0 0.00552 0.0287644 0.0484256 0.547619 Gammaproteobacter 0.90021 0.02323 0.03137 0.03325 0.04903 0.03205 0.01766 0.01693 0.00567 0.00368 0.2074178 0.0151994 0.031746 Spirochaetes 0.00226 0.00179 0 0 0 0 0.00161 0 0 0 0.0008098 0.0003212 0.440686 TM7-3 0.00226 0.00357 0 0 0.00213 0.10122 0.01124 0.0237 0.07372 0.00184 0.0015936 0.042344 0.0593271 Mollicutes 0.09952 0.15903 1.17522 0.33056 0.71846 0.08941 0.04657 0.00903 0.72962 0.00736 0.4965562 0.1763984 0.0952381 RF3 0 0 0 0 0 0 0 0.0158 0 0 0 0.003160.4237108 Opitutae 0.00226 0 0 0 0 0 0 0 0 0 0.0004524 0 0.4237108 Verrucomicrobiae 0.14928 0.21442 0.24885 0.75891 0.18548 0.52298 0.67124 1.03605 0.55194 0.27412 0.3113872 0.6112658 0.0952381 CCU21 0 0 0 0 0 0 0 0.00113 0 0 0 0.00022580.4237108 iii1-15 0.03167 0.00179 0.00837 0.00978 0 0 0 0.02709 0 0 0.0103196 0.0054172 0.1812205 Order Solibacterales 0.00679 0 0 0 0 0 0 0 0 0 0.001357 0 0.4237108 Sva0725 0 0 0.00837 0 0 0 0 0 0 0 0.001673 0 0.4237108 DS-18 0 0 0 0 0 0 0 0.00451 0 0 0 0.00090280.4237108 Ding N, et al.
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    ANALYSIS OF MICROBIAL COMMUNITY STRUCTURES AND FUNCTIONS IN HEAVY METAL-CONTAMINATED SOILS USING MOLECULAR METHODS THÈSE NO 2862 (2003) PRÉSENTÉE À LA FACULTÉ ENVIRONNEMENT NATUREL, ARCHITECTURAL ET CONSTRUIT Institut des sciences et technologies de l'environnement SECTION DES SCIENCES ET INGÉNIERIE DE L'ENVIRONNEMENT ÉCOLE POLYTECHNIQUE FÉDÉRALE DE LAUSANNE POUR L'OBTENTION DU GRADE DE DOCTEUR ÈS SCIENCES PAR Fabienne GREMION biologiste diplômée de l'Université de Neuchâtel de nationalité suisse et originaire de Gruyères (FR) acceptée sur proposition du jury: Prof. H. Harms, directeur de thèse Dr A. Chatzinotas, rapporteur Prof. A. Hartmann, rapporteur Prof. Ch. Holliger, rapporteur Dr F. Widmer, rapporteur Lausanne, EPFL 2003 SUMMARY The contamination of agricultural land and groundwater by heavy metals is essentially linked to human activities. A major problem with heavy metals is that they cannot be biodegraded and therefore reside in the environment for long periods of time if they are not removed. Thus, depending of the kind and depth of contamination, different remediation techniques were developed. One of these methods, called «phytoextraction», uses the ability of so-called hyperaccumulating plants to extract high amounts of heavy metals. Accumulation of heavy metals in the environment is a serious concern for animal and human health. At the microscopic scale, heavy metals may have also deleterious effects on bacteria which are the key-players of the different nutrient turnovers in soils. Consequently, ecosystem functioning can be seriously perturbed and the long-term soil fertility may be threatened. The recent development of molecular biology greatly contributed to the discovery of the microbial diversity and its function in the soil.
  • Sequence Analysis Allows Functional Annotation of Tyrosine Recombinases in Prokaryotic Genomes

    Sequence Analysis Allows Functional Annotation of Tyrosine Recombinases in Prokaryotic Genomes

    bioRxiv preprint doi: https://doi.org/10.1101/542381; this version posted February 6, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Title: Sequence analysis allows functional annotation of tyrosine recombinases in prokaryotic genomes. Authors: Georgy Smyshlyaev1,2, Orsolya Barabas2, Alex Bateman1 1European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL- EBI), Wellcome Genome Campus, Hinxton, UK 2European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany Corresponding author: Georgy Smyshlyaev Postdoctoral Fellow, Barabas Lab European Molecular Biology Laboratory Structural and Computational Biology Unit Meyerhofstraße 1 69117 Heidelberg, Germany T +49 6221 387-8645 E-mail: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/542381; this version posted February 6, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. ABSTRACT Background: Tyrosine recombinases perform site-specific genetic recombination in bacteria and archaea. They safeguard genome integrity by resolving chromosome multimers, as well as mobilize transposons, phages and integrons, driving dissemination of genetic traits and antibiotic resistance. Despite their abundance and genetic impact, tyrosine recombinase diversity and evolution has not been thoroughly characterized, which greatly hampers their functional classification. Results: Here, we conducted a comprehensive search and comparative analysis of diverse tyrosine recombinases from bacterial, archaeal and phage genomes.
  • The Impact of Urbanization on Soil Bacterial Diversity and Community Composition in Long Island, New York

    The Impact of Urbanization on Soil Bacterial Diversity and Community Composition in Long Island, New York

    The Impact of Urbanization on Soil Bacterial Diversity and Community Composition in Long Island, New York by KAUNG MYAT SAN Thesis submitted to the Graduate Faculty in Biology in fulfillment of the requirements for the degree of Master of Art, The City University of New York March 2019 Approved by: __________________________________ Date: _________________________________________ i TABLE OF CONTENT Thesis Approval Form………………………………………………………………… i-ii Abstract………………………………………………………………….……………… iii Acknowledgements……………………………………………………………………... iv Introduction……………………………………….……………………. ……………. 1-7 1.1 Urbanization 1.2 Soil profile 1.3 Role of Microbes in Soil 1.4 Soil Bacterial Diversity and pH is linked to Human Population Density in Urban Centers 1.5 The Effects of Soil pH on Bacterial Diversity and the community composition Objectives and Hypotheses…………………………………………………………. 8-12 Materials and Methods……………………………………………………………. 13-21 2.1 Environmental Soil Collection 2.2 Soil Characterization of pH 2.3 Metagenomic Methods 2.4 DNA Sequences Processing 2.5 Statistical Analysis Results ……………………………………………………………………………… 22-28 Discussion …………………………………………………………………………. 29-32 Supplementary Materials…………………………………………………………. 33-42 References…………………………………………………………………………. 43-44 i QUEENS COLLEGE Of THE CITY UNIVERSITY OF NEW YORK Thesis Approval Form Mr./Ms_________________________________________________________________ (Please Print) a candidate for the degree of Master of Art [ ] Master of Science in Education [ ] Has satisfactorily completed a Master’s thesis